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Ruth Lydia Schmidt

Microbial Ecologist & Data Scientist

A dynamic and resourceful microbial ecologist with 8 years of experience in
agricultural microbiome research, data analysis and science communication, strong leadership and a broad set of technical and interpersonal skills.
Passionate about finding sustainable solutions for pressing issues of our time through science, data and policy.

Education

Ph.D. in Microbial Ecology

Wageningen University & Netherlands Institute of Ecology
Title: Volatile communication between fungi and bacteria

Wageningen, The Netherlands

2017

M.S. in Biotechnology

Graz University of Technology

Graz, Austria

2012

M.S. in Molecular Biology

Graz University of Technology

Graz, Austria

2010

Research Experience

Mitacs Postdoctoral Fellow

Institut national de la recherche scientifique (INRS) & Plotly

Montréal, Canada

2020 - Present

  • Developing open-source visualization apps for omic data in microbiome research using Ploty’s Dash R and Dash Bio libraries.

Visiting JSPS Postdoctoral Fellow (short-term stay)

Kochi Core Center

Kochi, Japan

2020

  • Developed screening method for detection of terpene synthase genes (TPS) across terrestrial and aquatic environments.

Consultant

International Union for Conservation of Nature (IUCN)

remote

2019

  • Contributed to a global report on soil biodiversity in agro-ecosystem health.

Postdoctoral Fellow

Institut national de la recherche scientifique (INRS)

Montréal, Canada

2018 - 2020

  • Research on microbial solutions to drought in agriculture.
  • Led lab and field studies with wheat under drought conditions.
  • Conducted analysis of omic data (quantitative metagenomics, metatranscriptomics, metabolomics).

PhD Candidate

Netherlands Institute of Ecology & Wageningen University

Wageningen, The Netherlands

2013 - 2018

  • Studied microbial secondary metabolites for sustainable agriculture.
  • Characterized molecular mechanism underlying volatile interaction in soil microbes using a combination of omic, microbiological, and analytical (GC-MS) approaches.
  • Analyzed omic data (proteomics, metabolomics) and developed workflow for metabolomic data analysis.
  • Mentored 4 undergraduate and 1 graduate student on molecular biology research projects.
  • Collaborated with international research institutes in Germany, US & Sweden on genomics and proteomics projects.

Master student and University assistant

Graz University of Technology

Graz, Austria

2010-2012

  • Led and conducted field study on the effect of biocontrol agents in field in Egypt.
  • Performed analysis of 16S rRNA sequencing data & analytical data (LC-MS).

Teaching Experience

Supervisor of 2 PhD and 2 master students

Institut national de la recherche scientifique (INRS)

Montréal, Canada

2018 - Present

Teaching Assistant in Microbial Ecology field course

Wageningen University

Wageningen, The Netherlands

2016

Instructor in two days hands-on course on environmental proteomics

Netherlands Institute of Ecology

Wageningen, The Netherlands

2016

Supervisor of 3 Bachelor, 2 Master student & 1 PhD student

Wageningen University

Wageningen, The Netherlands

2014 - 2017

Teaching Assistant in Laboratory Course Environmental and Food Biotechnology

Graz University of Technology

Graz, Austria

2013

Research Assistant in Laboratory Course in Biochemistry and Molecular Biology

Karl-Franzens University

Graz, Austria

2012

Grants & awards

Mitacs Postdoctoral Fellowship (60,000 CAD)

Visualization of multi-omics data in microbiome research

Montréal, Canada

2019

Japan Society for the Promotion of Science (JSPS) Award (8,000 CAD)

Uncovering microbial chemical ecology in the extreme sub-seafloor environment

Kochi Core Centre, Japan

2019

Quebec Centre for Biodiversity Science (QCBS) Travel grant (1,500 CAD)

International Phytobiome meeting

Montpellier, France

2018

QCBS Seed grant (5,000 CAD)

Aural soilscapes: creating ecological consciousness to global warming

Montréal, Canada

2018

QCBS Travel grant (1,500 CAD)

ISME17 meeting

Leipzig, Germany

2018

International Society of Chemical Ecology (ISCE) Travel Grant (1,000 USD)

Annual Meeting ISCE17

Kyoto, Japan

2017

Best Talk Award (150 USD)

Annual Meeting ISCE17

Kyoto, Japan

2017

Federation of European Microbiological Societies (FEMS) Research Grant (5,000 Eur)

Research on fungal genomics at the Swedish University of Agricultural Sciences (SLU)

Uppsala, Sweden

2017

International Society for Microbial Ecology (ISME) Travel Grant (800 Eur)

ISME16 meeting

Montréal, Canada

2016

FEMS Meetings Attendance Grant (300 Eur)

Ecology of Soil Microorganisms meeting

Prague, Czech Republic

2015

Best Poster Award (100 Eur)

Ecology of Soil Microorganisms meting

Prague, Czech Republic

2015

Presentations

Kochi Core Center (talk)

Uncovering microbial terpenes in the extreme sub-seafloor environment.

Kochi, Japan

2020

International Society of Chemical Ecology, ISCE 35 (talk)

Microbial chemical ecology: past, present and future.

Atlanta, USA

2019

Second International Holobiont meeting (talk)

How microbial volatiles help plants survive in times of drought.

Montréal, Canada

2019

QCBS Symposium (talk)

Microbial aromas might help plants survive drought.

Montréal, Canada

2018

International Phytobiome meeting (poster)

Microbial terpenes in the plant holobiont as a mechanism to adapt to drought.

Montpellier, France

2018

International Symposium on Microbial Ecology, ISME 17 (talk)

Do bacteria and fungi have a fragrant language all their own?

Leipzig, Germany

2018

Champalimaud Centre for the Unknown

Microworld - the most powerful life on earth.

Lisbon, Portugal

2018

International Society of Chemical Ecology, ISCE 17 (talk)

Terpenes as lingua franca between fungi and bacteria.

Kyoto, Japan

2017

International Symposium on Microbial Ecology, ISME 16 (poster)

Volatile conversations between fungi and bacteria.

Montréal, Canada

2016

Ecology of soil microorganisms, ESM (poster)

Microbial small talk: Volatiles in fungal-bacterial interactions.

Prague, Czech Republic

2015

4th International student conference on Microbial Communication, MiCom (talk)

Chemical dialogues: The ability of bacteria to sense fungal volatiles.

Jena, Germany

2014

CNRS-Jacques Monod conference: bacterial–fungal interactions: a federative field for fundamental and applied microbiology

The role of fungal volatiles as signaling compounds in bacterial-fungal interactions.

Roscoff, France

2013

Boston Bacterial Meeting, BBM (poster)

Microbial interactions via secondary metabolites in soil.

Boston, USA

2013

Netherlands Annual Ecology Meeting, NERN (poster)

The best bacterial competitive strategies in the rhizosphere.

Lunteren, The Netherlands

2013

Publications

A Gaseous Milieu: Extending the Boundaries of the Rhizosphere.

Trends in microbiology. DOI: 10.1016/j.tim.2020.02.016

N/A

2020

de la Porte, A., Schmidt, R., Yergeau, É., & Constant, P.

Microbe-driven chemical ecology: past, present and future.

ISME J. DOI: 10.1038/s41396-019-0469-x

N/A

2019

Schmidt, R., Ulanova, D., Wick, L. Y., Bode, H. B., & Garbeva, P.

Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum.

FEMS Microbiol Ecol. DOI: 10.1093/femsec/fiy078

N/A

2018

Schmidt, R., Durling, M. B., de Jager, V., Menezes, R. C., Nordkvist, E., Svatoš, A., Dubey, M., Lauterbach, L., Dickschat, J. S., Karlsson, M., & Garbeva, P.

Fifty Percent Human - how art brings us in touch with our microbial cohabitants.

Microb Biotechnol.DOI: 10.1111/1751-7915.13285

N/A

2018

Bäumel, S., Tytgat, H., Nemec, B., Schmidt, R., Chia, L. W., & Smidt, H.

The future of ecology is collaborative, inclusive and deconstructs biases.

Nat Ecol Evol. DOI: 10.1038/s41559-017-0445-7

N/A

2018

Ramirez, K. S., Berhe, A. A., Burt, J., Gil-Romera, G., Johnson, R. F., Koltz, A. M., Lacher, I., McGlynn, T., Nielsen, K. J., Schmidt, R., Simonis, J. L., terHorst, C. P., & Tuff, K. Scientific reports.

Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C.

Sci Rep. DOI: 10.1038/s41598-017-00893-3

N/A

2017

Schmidt, R., Jager, V., Zühlke, D., Wolff, C., Bernhardt, J., Cankar, K., Beekwilder, J., Ijcken, W. V., Sleutels, F., Boer, W., Riedel, K., & Garbeva, P.

Controlling the Microbiome: Microhabitat Adjustments for Successful Biocontrol Strategies in Soil and Human Gut.

Front Microbiol. DOI: 10.3389/fmicb.2016.01079

N/A

2016

Adam, E., Groenenboom, A. E., Kurm, V., Rajewska, M., Schmidt, R., Tyc, O., Weidner, S., Berg, G., de Boer, W., & Falcão Salles, J.

Microbial Small Talk: Volatiles in Fungal-Bacterial Interactions.

Front Microbiol. DOI: 10.3389/fmicb.2015.01495

N/A

2016

Schmidt, R., Etalo, D. W., de Jager, V., Gerards, S., Zweers, H., de Boer, W., & Garbeva, P.

Volatile affairs in microbial interactions.

ISME J. DOI: 10.1038/ismej.2015.42

N/A

2016

Schmidt, R., Cordovez, V., de Boer, W., Raaijmakers, J., & Garbeva, P.

Exploring the genomic traits of fungus-feeding bacterial genus Collimonas.

BMC Genomics. DOI: 10.1186/s12864-015-2289-3

N/A

2015

Song, C., Schmidt, R., de Jager, V., Krzyzanowska, D., Jongedijk, E., Cankar, K., Beekwilder, J., van Veen, A., de Boer, W., van Veen, J. A., & Garbeva, P.

Effects of bacterial inoculants on the indigenous microbiome and secondary metabolites of chamomile plants.

Front Microbiol. DOI: 10.3389/fmicb.2013.00400

N/A

2014

Schmidt, R., Köberl, M., Mostafa, A., Ramadan, E. M., Monschein, M., Jensen, K. B., Bauer, R., & Berg, G.

The microbiome of medicinal plants: diversity and importance for plant growth, quality and health.

Front Microbiol. DOI: 10.3389/fmicb.2014.00064

N/A

2013

Köberl, M., Schmidt, R., Ramadan, E. M., Bauer, R., & Berg, G.

Manuscripts in preparation

Soil hydrogen enrichment increases H2-oxiding bacterial activity and changes microbial community structure and function (under review).

Soil Biol. Biochem.

N/A

N/A

Wang X., Schmidt R., Constant P., & Yergeau E.

Nitrapyrin has far reaching effects on the soil microbial community structure, composition, diversity and functions (submitted).

Appl. Environ. Microbiol.

N/A

N/A

Schmidt R., Wang X., Garbeva, P., & Yergeau E.

Infochemicals in terrestrial plants and marine macroalgal holobionts under a changing climate (under review).

New Phytologist.

N/A

N/A

Schmidt R., & Saha, M.

Press and Outreach (EXCERPT)

The Art of Microbial Communication.

SciArt Magazine.

N/A

2018

References upon request